RnoINT0070928 @ rn6
Intron Retention
Gene
ENSRNOG00000009341 | Hivep3
Description
human immunodeficiency virus type I enhancer binding protein 3 [Source:RGD Symbol;Acc:1311252]
Coordinates
chr5:139071088-139074725:+
Coord C1 exon
chr5:139071088-139071998
Coord A exon
chr5:139071999-139072987
Coord C2 exon
chr5:139072988-139074725
Length
989 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TGTTTTTCTGTCTCCTCCAGAAG
3' ss Score
11.44
Exon sequences
Seq C1 exon
GAACCAGTGACGACCTACTCCAGGACTCAGAGGGGCGAGAGGGCTCCGAAGCTGTGGAGGAGCACCAGTTTTCAGACCTGGAGGACTCTGACTCAGACTCAGACCTGGATGAAGATGAAGAGGAGGAGGAGGAGGAGGAAGAGGAGAGCCAGGATGAGCTGTCCAGGCCATCCTCAGAGGCAGCTCCACTCTGCCTGCCAGCCACACTACAGGAGGACTCCTCCCTGATTCGGGGCCCTCAGCCTCCAGATGCCACTTCAGACGCGGCCCCACGAGGCAGCTCCATCTCAGAAGCCACGCGTCTGACAGCCAGCAGCTGTTCCACACCCAGCCAGGGTACCCAAGGCCTTCCTCGGCTGGGACTGGCCCCACTGGAGAAAGGCACGAGCTCAGCCCTGAGTCCCAAGGCCACATCCCCTAGGAGGCCGTGGTCCCCAAGCAAAGAAGCAGGCAGCCGCCCCTCACTCACTCGCAAACATTCACTCACCAAAACCGACTCATCTCCCCAGCGATGTTCACCGGCCCGAGCTCAGGCCTCAGTCGCGAGCACACCTGGTCCCCAGACGGGCCCAGGAAGGGACCTAAGTCCTCACCTTTGTGGGTCTCCGAGACCAGAGTTGTCCTGTCTGACTCCCTACCCCATAGGAAGAGAGGTGCCCGCTGGACTTGAGAGTGCCACAGTCACAGGCACCCCCAGATGTTCACCCACCAGGAGACGGTCCCTGGGTCGGGCCGAGTCATCGCCGCCGCACACAGTGCTGCCGGGGACGTGGGCCCTAGGTGGGCCCTGCAGCCCCTCAGTGGACAAGTATGGCCTGGGCTTGGGGCCGGTTCCACGGGCTCTCCTCCAGCCCGTGCCTCTACCTCACACACTTCTCAGCAGAAGCCCGGAAACGTGCGCCTCTGCATGG
Seq A exon
GTGAGTCCTGGGGGGTCAGGAGCTCCCCATCCACACCGTCCGCACCTCACGTCCACACCTGGCCGGCGTTCCTGGTCTTATAGCGAGCATTTCCTGGGTCCCCACTCTACCAGCCAGTTTATTGCACTTGGAGGCACCCTCAGAAGCCCCGAACATGACTCTGGTGTTCGCCAGCTCTAGCCCTAGCAGGCAGGGTACGGGAGGATGTGGATGTAAACACTTGTATAGTCCTTCAGCCATCCCTTCCCTGTCTACGTGTGTCCTTGGAGCAGGTGACAGACAGCTTTACCAAAACCATCAGTCCCCATCTCCTTCATGAACATCACAGTCCACACCATCCCTGTGGAACCATGAGTGCAGTGGTTGAAGCAACCTTGCCTCAGTCACCACCGTGCCCTACCACACCACCACTAGTGCTGACCACCACCACCACCACCACCCGCAATATCGTTTCATCATCTACACTGTCCCTGTCCTGGTGCCTTGCAGTGTCTGTACCGCTACCACAGTGCCTCCTGTGGCTGCCACTGCCCAAGGCTGGCCCTGTCCCTGTGAACATTGCTTGCATTGTGTTGTCAGGACCCCACAGCATCTCTCCTGGAGGAACATTGACTAAAGTATCTTTCTTGCCACATTGAACTTCCTGTAGTGGAAGGTGGAAATCCTTGGGTGGGAATTCATATGCAAGGGTGAAGTTAGGCCAAGACCATTTTAAGAAGGGGTGAGGCAGAAGAGCCAAGGTAAACCAGGGCAACCACAGATCCCCATTCCCAGGAGCCGCCTCCTACAGATATGGGCCAGCATGTCCCTCTAAGTTTCCCAGTAGGAAGCTCCTTGAGCACAGCATTAGGACTCCTGATTCTGGCCATACTCACCAGCCTTACTCTGACCTCAGGCCTCCCTGCCCTCTATAACTCTAGCCCTAAGTCCTGCAGATGCCCAGCATGTAACCCTTGTCTTCTCCTGTTTTGTTTTTCTGTCTCCTCCAG
Seq C2 exon
AAGACTGAATCCCGAAGTCCATCAGCTGGTCCTGCTCCTCTCTCTTCCCGACCATCCTCTGCCCCTCATGACTTCCACGGCCACCTCCCTAGCCGAAGTGAGGAGAACCTCTTCAGCCACCTGCCTCTGCATTCCCAGCACCTGAATCGCACCCCCTGCCCCCTCATTCCCATCGGTGGGATCCAAATGGTACAGGCCCGACCAGGAGCCCACCCCACCCTGCTGTCAGGACCCTGTGCAGCCTGGGTCAGTGGCTTCTCAGGGGGTGGCAGTGACCTAACTGGGGCCCGAGAGGCCCAGGAGCGCAGCCGCTGGAGTCCCACGGAGAGCCCTTCAGCATCAGTGTCCCCTGTGGCCAAGGTCTCCAAGTTTACACTCTCTTCAGAGCTGGAGGAGGAAAGGACCAGCCGAGGCCCAGGAAGACCTCCTGCCTGGGAACCTCACAGGGCTGAAGCCCCTGCAGAAACCATGGGCACACACAGCCCCTGCCCCCCACAGCTGCCCCAAGGGCACCCGCTGGCACCATCCTGGAGGGGCCTCCTGGAATCACCACACGCACTGGCCAACCTAAAGGCCTCAAGCTTCCCGCCACTGGACCGCAGCAGCTCCATGGACTGCCTGGCAGAGACCTCCACTTGCTTTCCACCCCGGAGCAGGAACCTCTCTGGAGAACCCAGGACCCGCCCAGACTCCCCTGAGCTCTTAGGTAGTGGGGAGCTCAGGACACCTCTATTCCTGTCCAAGGATAGCGGCCCCCCAAGCATCTAAGCCTCTGCAGTACTTCAGCACTGGCCTCAGTGTTCGGCAGCAGACACTTCCTGCCAACCGCCTGGAGTCATACTGCTCCCGCGGGCATCCTCTCCCATCTGTCCATCTGTCCATCTGTCCATGCAGCTTCTGCTCAGCCCCGTCTGTTCTATTTTTCCACATATGCAGTTACCTGTGCCTTTTTCTAGACCTTTTGTTGCTTGAAAAAAAAATCACACACATCCATAAACGAAACGAAACAAACACATCCACGAGGAGCTCTAGGCTGTGAGTAGTTTGTGCTCTGGGGACAAGGCTGGAGGAGGGACTCTCCACCTCCACCACCACATGCCGTACTGGCAGCCGTCCCCACCTCAAGGTCCCTGAGAGAGAGGGTCTATTGCACTGAGAGAGAAGAAAGGGGGAGAAAAATATAATTAAATTCAAAGGCAAGCACTCCTACAGACAGATTCCCAAGATCCCCACTCATAACACATACGGTTCATAGCCACCCCGCTCTGCCATCAGAGGAACCAGAACCCCAAAGCAGGACACAAATACAGGCAGGAACCAACCCGCTACTCCCCACCCTACCTAGCTAAGAACATTATCTTTTATCCTATGTAGTGTGAACCAAGCTCTCACCTTCTCCCTTCCTTACTCCACCTCCGCCCAGGGCTTGCCCATCTGTCTCCTTTCTCCTACACACTGTAGGTCTCTGCCTCCTGGGCCTGGCCACACGCTGGCTCCTTTATGTTCAGAAATACCCACAGGATGGAGGGGCCAAGGCAGGACTAGGGATGGTCCTAGTCTGGACCTGTTCTGAGCCTGGAGTTTGGATTCTGTTTCACCTGTGGCCCTGAGACAGCACATCACACTTCCTTCCTGGCAGGATTGACGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATACACACAGAGAGAAACCAAAGATGGTGCTTGGTACTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009341:ENSRNOT00000066774:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.901 A=NA C2=0.894
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCCCATAGGAAGAGAGGTGC
R:
GAAGTCATGAGGGGCAGAGGA
Band lengths:
350-1339
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]